Finished Citadel, got fragments, map completed, but not on atlas

So I found my second citadel today. After killing the boss and all rares, the map said it was complete, and I got my fragments and left the map.

I went to put the next map in, and noticed it said the citadel was still in progress, and I couldn't open the next map attached to it. Upon going back in the map, it now said that the map wasn't complete.

Once I opened another map, I could no longer enter the citadel, and it said I failed it even though it was completed.

Not sure if it matters which citadel it was, but it was the Iron Citadel in this case.